NAME

BioX::Map - map read to genome with bwa and soap

VERSION

version 0.0.12

SYNOPSIS

  use BioX::Map;
  my $bm = BioX::Map->new(
    infile      => "in.fastq",
    out_prefix  => 'out',
    genome      => 'ref.fa',
  );

DESCRIPTION

This module aim to wrap bwa and soap, and statistic result

Attributes

infile

the fastq file

indir

The dir that include fastq file. The priority is higher than infile

outfile

path of outfile which could include path

outdir

outdir of mapping result

force_index

index genome before mapping

mismatch

set mismatch allowed in mapping

genome

path of genome file

tool

mapping software. Enum['bwa', 'soap']

bwa

path of bwa

soap

path of soap

soap_index

path of 2bwt-builder

process_tool

process of mapping software

process_sample

how many samples are processed parallel

METHODS

exist_index

check whether genome index exists

create_index

create genome index before mapping

_map_one

wrap mapping software

map

process one or more samples

statis_result

statis mapping result

AUTHOR

Yan Xueqing <yanxueqing621@163.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2016 by Yan Xueqing.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.